Question: annaffy-like HTML autput for org.Hs.eg.db and similar metadata packages
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gravatar for Claudio Lottaz
9.2 years ago by
Claudio Lottaz40 wrote:
Dear all, I lately used annaffy on a regular basis to generate HTML-output for gene lists from Affymetrix microarray analysis. I now also need similar output from annotation data taken from org.Hs.eg.db and similar packages. Unfortunately, annaffy has difficulties to cope at least with GO and cytobands as far as I can see. Does anybody happen to know some workarounds here? Thanks for any help! Cheers, Claudio -- ------------------------------------------------------ Claudio Lottaz Computational Diagnostics, Institute for Functional Genomics University of Regensburg, D-93053 Regensburg (Germany) phone: +49 941 943 1584, fax: +49 941 5020
ADD COMMENTlink modified 9.2 years ago by Vincent J. Carey, Jr.6.3k • written 9.2 years ago by Claudio Lottaz40
Answer: annaffy-like HTML autput for org.Hs.eg.db and similar metadata packages
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gravatar for Vincent J. Carey, Jr.
9.2 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
You aren't providing useful details, but I have observed the problem you mention. Since aafTableAnn("1000_at", "hgu133plus2.db") works nicely, one would hope that the semantically unrelated aafTableAnn("1000", "org.Hs.eg.db") might do something nice too. What happens? > aafTableAnn("1000", "org.Hs.eg.db") Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) : object 'org.Hs.egORGPKG' not found If we read some doc and thrash around a little bit we find > aafTableAnn("1000", "org.Hs.eg.db", colnames="Symbol") An object of class "aafTable" Slot "probeids": [1] "1000" Slot "table": $Symbol An object of class "aafList" [[1]] [1] "CDH2" attr(,"class") [1] "aafSymbol" So some mapping can be carried out (with translation to hyperlinked HTML by the usual approaches for some fields) In fact, it seems aafTableAnn("1000", "org.Hs.eg.db", colnames=aaf.handler()[-c(11)]) will obtain all the usual mappings except GO. If we look at aafGO we find that it will issue queries regarding a table named probes, but such a table only exists in the affy annotation packages, not in org.Hs.eg.db. It would be nice to extend annaffy's functionality more broadly -- it works, IIRC, with any chip-oriented product of the AnnotationDbi SQLforge (e.g., for illumina arrays), but not with the org.* packages. > sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-03 r51901) x86_64-apple-darwin10.3.0 locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] hgu133plus2.db_2.4.1 org.Hs.eg.db_2.4.1 annaffy_1.21.0 [4] KEGG.db_2.4.1 GO.db_2.4.1 RSQLite_0.8-4 [7] DBI_0.2-5 AnnotationDbi_1.11.0 Biobase_2.9.0 [10] weaver_1.15.0 codetools_0.2-2 digest_0.4.2 On Wed, May 5, 2010 at 8:50 AM, Claudio Lottaz < Claudio.Lottaz@klinik.uni-regensburg.de> wrote: > Dear all, > > I lately used annaffy on a regular basis to generate HTML-output for gene > lists from Affymetrix microarray analysis. I now also need similar output > from annotation data taken from org.Hs.eg.db and similar packages. > Unfortunately, annaffy has difficulties to cope at least with GO and > cytobands as far as I can see. Does anybody happen to know some workarounds > here? > > Thanks for any help! > Cheers, > Claudio > > > > -- > ------------------------------------------------------ > Claudio Lottaz > Computational Diagnostics, Institute for Functional Genomics > University of Regensburg, D-93053 Regensburg (Germany) > phone: +49 941 943 1584, fax: +49 941 5020 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 9.2 years ago by Vincent J. Carey, Jr.6.3k
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